Plant-based recombinant protein manufacturing systems that employ viral expression vector technologies can quickly and inexpensively produce large amounts of high quality proteins for pharmaceutical and other uses. When purifying recombinant proteins produced in plants infected with these virus-based gene expression systems, high concentrations of virus particles and viral coat protein are typically present in the homogenate and subsequent product stream. Removal of these impurities can be time-consuming and costly. Several approaches have been applied to remove virus from plant extracts, including pH and temperature shifts, ultrafiltration, and combinations thereof. However, these strategies are not always compatible with the biochemical properties of the product and, since their efficiencies vary, additional downstream virus removal steps may still be required. With each successive step in a purification process, the quantity of recovered product decreases and the overall costs of the process tend to increase. Removing virus and coat protein impurities at an early stage would be expected to relieve the burden on downstream separation steps and help to control purification costs. Additionally, diminishing the infective potential of the virus would serve as an internal safeguard against accidental release of the recombinant virus into the environment.